They should check for free space on arrival rather than just when the order is sent.

I'm not sure the auton can be prevented from gating without significant changes, but it could be redeployed and send an error message if there's no free space in <OnEnteredGate>.

megas 1 Jun 2016:

Redeploying a new copy immediately after gating is probably the easiest solution. This solution was used in some mods. Another alterative solution: items could be unpacked and the excess auto-dropped in a crate.

nms 15 Aug 2017:

I added code to fix this in 1.8a2.